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bioconductor-bsgenome.hsapiens.ucsc.hg18.masked
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public |
Full genome sequences for Homo sapiens (Human) as provided by UCSC (hg18, Mar. 2006) and stored in Biostrings objects. The sequences are the same as in BSgenome.Hsapiens.UCSC.hg18, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.
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2024-12-31 |
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bioconductor-vanillaice
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public |
A Hidden Markov Model for high throughput genotyping arrays
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2024-12-31 |
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bioconductor-bsgenome.cfamiliaris.ucsc.canfam2.masked
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public |
Full genome sequences for Canis lupus familiaris (Dog) as provided by UCSC (canFam2, May 2005) and stored in Biostrings objects. The sequences are the same as in BSgenome.Cfamiliaris.UCSC.canFam2, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.
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2024-12-31 |
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bioconductor-bsgenome.sscrofa.ucsc.susscr3.masked
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public |
Full genome sequences for Sus scrofa (Pig) as provided by UCSC (susScr3, Aug. 2011) and stored in Biostrings objects. The sequences are the same as in BSgenome.Sscrofa.UCSC.susScr3, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.
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2024-12-31 |
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bioconductor-flowsorted.blood.epic
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public |
Illumina EPIC data on immunomagnetic sorted peripheral adult blood cells
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2024-12-31 |
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bioconductor-tfbstools
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public |
Software Package for Transcription Factor Binding Site (TFBS) Analysis
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2024-12-31 |
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bioconductor-hdf5array
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public |
HDF5 datasets as array-like objects in R
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2024-12-31 |
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bioconductor-bsgenome.drerio.ucsc.danrer6.masked
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public |
Full genome sequences for Danio rerio (Zebrafish) as provided by UCSC (danRer6, Dec. 2008) and stored in Biostrings objects. The sequences are the same as in BSgenome.Drerio.UCSC.danRer6, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.
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2024-12-31 |
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bioconductor-bsgenome.ggallus.ucsc.galgal4.masked
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public |
Full genome sequences for Gallus gallus (Chicken) as provided by UCSC (galGal4, Nov. 2011) and stored in Biostrings objects. The sequences are the same as in BSgenome.Ggallus.UCSC.galGal4, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.
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2024-12-31 |
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bioconductor-bsgenome.btaurus.ucsc.bostau4.masked
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public |
Full genome sequences for Bos taurus (Cow) as provided by UCSC (bosTau4, Oct. 2007) and stored in Biostrings objects. The sequences are the same as in BSgenome.Btaurus.UCSC.bosTau4, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.
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2024-12-31 |
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bioconductor-bsgenome.drerio.ucsc.danrer7.masked
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public |
Full genome sequences for Danio rerio (Zebrafish) as provided by UCSC (danRer7, Jul. 2010) and stored in Biostrings objects. The sequences are the same as in BSgenome.Drerio.UCSC.danRer7, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.
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2024-12-31 |
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bioconductor-cleanupdtseq
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public |
cleanUpdTSeq cleans up artifacts from polyadenylation sites from oligo(dT)-mediated 3' end RNA sequending data
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2024-12-31 |
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bioconductor-bsgenome.mmusculus.ucsc.mm9.masked
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public |
Full genome sequences for Mus musculus (Mouse) as provided by UCSC (mm9, Jul. 2007) and stored in Biostrings objects. The sequences are the same as in BSgenome.Mmusculus.UCSC.mm9, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.
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2024-12-31 |
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bioconductor-bsgenome.cfamiliaris.ucsc.canfam3.masked
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public |
Full genome sequences for Canis lupus familiaris (Dog) as provided by UCSC (canFam3, Sep. 2011) and stored in Biostrings objects. The sequences are the same as in BSgenome.Cfamiliaris.UCSC.canFam3, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.
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2024-12-31 |
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bioconductor-bsgenome.ggallus.ucsc.galgal3.masked
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public |
Full genome sequences for Gallus gallus (Chicken) as provided by UCSC (galGal3, May 2006) and stored in Biostrings objects. The sequences are the same as in BSgenome.Ggallus.UCSC.galGal3, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.
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2024-12-31 |
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bioconductor-bsgenome.amellifera.ucsc.apimel2.masked
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public |
Full genome sequences for Apis mellifera (Honey Bee) as provided by UCSC (apiMel2, Jan. 2005) and stored in Biostrings objects. The sequences are the same as in BSgenome.Amellifera.UCSC.apiMel2, except that each of them has the 3 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), and (3) the mask of repeats from RepeatMasker (RM mask). Only the AGAPS and AMB masks are "active" by default.
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2024-12-31 |
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bioconductor-hireadsprocessor
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public |
Functions to process LM-PCR reads from 454/Illumina data
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2024-12-31 |
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bioconductor-bsgenome.mmusculus.ucsc.mm8.masked
|
public |
Full genome sequences for Mus musculus (Mouse) as provided by UCSC (mm8, Feb. 2006) and stored in Biostrings objects. The sequences are the same as in BSgenome.Mmusculus.UCSC.mm8, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.
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2024-12-31 |
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bioconductor-bsgenome.rnorvegicus.ucsc.rn4.masked
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public |
Full genome sequences for Rattus norvegicus (Rat) as provided by UCSC (rn4, Nov. 2004) and stored in Biostrings objects. The sequences are the same as in BSgenome.Rnorvegicus.UCSC.rn4, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.
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2024-12-31 |
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bioconductor-bsgenome.hsapiens.ucsc.hg17.masked
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public |
Full masked genome sequences for Homo sapiens (UCSC version hg17)
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2024-12-31 |
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bioconductor-bsgenome.mmulatta.ucsc.rhemac3.masked
|
public |
Full genome sequences for Macaca mulatta (Rhesus) as provided by UCSC (rheMac3, Oct. 2010) and stored in Biostrings objects. The sequences are the same as in BSgenome.Mmulatta.UCSC.rheMac3, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.
|
2024-12-31 |
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bioconductor-bsgenome.dmelanogaster.ucsc.dm2.masked
|
public |
Full genome sequences for Drosophila melanogaster (Fly) as provided by UCSC (dm2, Apr. 2004) and stored in Biostrings objects. The sequences are the same as in BSgenome.Dmelanogaster.UCSC.dm2, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.
|
2024-12-31 |
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bioconductor-bsgenome.ptroglodytes.ucsc.pantro2.masked
|
public |
Full genome sequences for Pan troglodytes (Chimp) as provided by UCSC (panTro2, Mar. 2006) and stored in Biostrings objects. The sequences are the same as in BSgenome.Ptroglodytes.UCSC.panTro2, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.
|
2024-12-31 |
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bioconductor-ensdb.rnorvegicus.v79
|
public |
Exposes an annotation databases generated from Ensembl.
|
2024-12-31 |
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bioconductor-ensdb.rnorvegicus.v75
|
public |
Exposes an annotation databases generated from Ensembl.
|
2024-12-31 |
|
bioconductor-ensdb.mmusculus.v75
|
public |
Exposes an annotation databases generated from Ensembl.
|
2024-12-31 |
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bioconductor-ensdb.hsapiens.v86
|
public |
Exposes an annotation databases generated from Ensembl.
|
2024-12-31 |
|
bioconductor-ensdb.hsapiens.v79
|
public |
Exposes an annotation databases generated from Ensembl.
|
2024-12-31 |
|
bioconductor-ensdb.hsapiens.v75
|
public |
Exposes an annotation databases generated from Ensembl.
|
2024-12-31 |
|
bioconductor-ensdb.mmusculus.v79
|
public |
Exposes an annotation databases generated from Ensembl.
|
2024-12-31 |
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bioconductor-scrnaseq
|
public |
Collection of Public Single-Cell RNA-Seq Datasets
|
2024-12-31 |
|
bioconductor-clipper
|
public |
Gene Set Analysis Exploiting Pathway Topology
|
2024-12-31 |
|
bioconductor-ruvseq
|
public |
Remove Unwanted Variation from RNA-Seq Data
|
2024-12-31 |
|
bioconductor-minfi
|
public |
Analyze Illumina Infinium DNA methylation arrays
|
2024-12-31 |
|
bioconductor-agimicrorna
|
public |
Processing and Differential Expression Analysis of Agilent microRNA chips
|
2024-12-31 |
|
bioconductor-affycoretools
|
public |
Functions useful for those doing repetitive analyses with Affymetrix GeneChips
|
2024-12-31 |
|
bioconductor-reportingtools
|
public |
Tools for making reports in various formats
|
2024-12-31 |
|
bioconductor-chipseq
|
public |
chipseq: A package for analyzing chipseq data
|
2024-12-30 |
|
bioconductor-girafe
|
public |
Genome Intervals and Read Alignments for Functional Exploration
|
2024-12-30 |
|
bioconductor-chipseqr
|
public |
Identifying Protein Binding Sites in High-Throughput Sequencing Data
|
2024-12-30 |
|
bioconductor-fastqcleaner
|
public |
A Shiny Application for Quality Control, Filtering and Trimming of FASTQ Files
|
2024-12-30 |
|
bioconductor-amplican
|
public |
Automated analysis of CRISPR experiments
|
2024-12-30 |
|
bioconductor-cner
|
public |
CNE Detection and Visualization
|
2024-12-30 |
|
bioconductor-shortread
|
public |
FASTQ input and manipulation
|
2024-12-30 |
|
bioconductor-rhdf5
|
public |
R Interface to HDF5
|
2024-12-30 |
|
bioconductor-inspect
|
public |
Modeling RNA synthesis, processing and degradation with RNA-seq data
|
2024-12-30 |
|
bioconductor-imas
|
public |
Integrative analysis of Multi-omics data for Alternative Splicing
|
2024-12-30 |
|
bioconductor-glmsparsenet
|
public |
Network Centrality Metrics for Elastic-Net Regularized Models
|
2024-12-30 |
|
bioconductor-rtcgatoolbox
|
public |
A new tool for exporting TCGA Firehose data
|
2024-12-30 |
|
bioconductor-eupathdb
|
public |
Brings together annotation resources from the various EuPathDB databases (PlasmoDB, ToxoDB, TriTrypDB, etc.) and makes them available in R using the AnnotationHub framework.
|
2024-12-30 |
